QIIME produces several files that can be analyzed in the phyloseq-package, This includes the map-file, which is an important input to QIIME that can also indicate sample covariates. It is converted naturally to the sample_data component data type in phyloseq-package, based on the R data.frame.
(Required). A character string or connection.
That is, any suitable
import_qiime for more information about QIIME. It is also the
suggested function for importing QIIME-produced data files.